The subject matter disclosed herein relates to image analysis of biological samples. More particularly, the disclosed subject matter relates to a modular region-level image analysis technique that is capable of being configured or modified depending on the sample type or the desired analysis outputs.
Various methods may be used in biology and in medicine to observe different targets in a biological sample. For example, analysis of proteins in histological sections and other cytological preparations may be performed using the techniques of histochemistry, immunohistochemistry (IHC), or immunofluorescence. Such analysis may be performed on acquired images that are stained with probes specific for biomarkers of interest. Once acquired, the images may be analyzed by a variety of techniques
In certain analysis techniques, segmentation is used to identify regions and/or units for biomarker quantification and feature extraction (e.g. morphological features). For example, a single cell segmentation analysis involves cell segmentation, cell level quantification and data analysis. The cell segmentation step uses multiple structural markers to segment the different subcellular compartments and then to delineate individual cell borders. This segmentation approach is called whole cell segmentation. In the second step, each biomarker is quantified at the cell level (e.g. mean or total for each cell) and at the subcellular level. Then, these cell level measurements are usually aggregated at the image or subject level at the beginning of the data analysis stage. While whole cell segmentation facilitates performing detailed cell level quantitation, such techniques have some drawbacks. For example, cell segmentation errors may result in quantification errors. In addition, detailed cell segmentation and cell level quantification of an image may be time consuming where the processing time may vary between images depending on tissue characteristics and the number of cells in the image. In addition, manual review of cell segmentation is also time-consuming. Further, cell level quantification does not easily capture tissue level properties (e.g. structural features).